I'm just ripping my normal Blu Rays. I'm sure it has all the audio tracks. 5.1, 7.1, 9.1, Dolby Atmos. Not sure about the audio conversion by MakeMKV, I just set it to rip & let it go. Never knew about any other options.

If you haven't changed your profile yet (if you don't know what that means, you haven't), there should be no conversion of the audio, other than, if you have a DTS-HD MA track, MakeMKV will optionally create a second track that only contains the "lossy" part of the DTS-HD, for compatibility. It also does this with True-HD, copying the "lossy" portion to a standard AC3 track.